Strange results when running graph and writing to GeoTiff

johngan · February 19, 2019, 3:12pm

I am working on a project related to land cover classification. I use Support Vector Machine (SVM) as classification algorithm. In order to improve the results, i also incorporate texture analysis (GLCM) into my code. Due to the fact that texture analysis is so slow using python, i decided to take advance of GPT in SNAP for performance purposes. So, for automating the whole classification pipeline, i created bash script which calls the SVM python script and the GLCM-PCA graph i constructed using SNAP (first GLCM-PCA is calculated using the graph and the results of GLCM are fed into the classifier).

The problem is the following:
I need the final GLCM results to be in GeoTIFF format (so that it can be loaded into my python code) as i set up my algorithm to work with data of that format. So, in the graph shown bellow change the formatNameinto GeoTIFF format.

Once, i run the graph, it works fine and i get the following results.

We see that, i tried three different format outputs. All formats work fine apart from geotiff. When loading the final GLCM (geotif) file into SNAP i get the image shown on the far right. I do not know whether anyone has come across with a similar issue.

So, someone might ask, why do not you use any of the other two formats?

NETCDF: firstly, my code has been set up to use geotiff format where i am more familiar with (it’s not huge problem to switch to netcdf I guess)
Big GeoTIFF: big geotiff produce files of larger size compared to geotiff. I would like to keep the size of the files to the minimum.

thanks

snasonova · February 19, 2019, 6:10pm

That happened to me too! I just used GeoTIFF-BigTIFF

johngan · February 20, 2019, 9:19am

Right, I am just hopping that, there might be a solution to that. Otherwise, i will have to use Big GeoTIFF

qglaude · February 20, 2019, 9:49am

Tiff is an uncompressed image file format that rapidly becomes big with large areas. In addition, Tiff files are limited to 4Gb maximum. Maybe that causes your issue?

johngan · February 20, 2019, 11:33am

Yes, tiff format is limited to 4GB as you mentioned.
When i do the whole process manually in SNAP and export the file in geotiff, the size of the raster is 500MB.
So, my raster size is not as big

I only get these weird results when using the graph to automate my pipeline and specify 'geotiff` format on the write operator

marpet · February 25, 2019, 9:35am

This is really a strange result.

Actually the size should not in crease when switching to BIG-GeoTIFF, at least not much. And for Big-GeoTiff compression can be enabled.
If you want to try it, add

snap.dataio.bigtiff.compression.type=LZW

to the snap.properties file in the etc folder of the SNAP installation directory (You need admin rights).

Back to your GeoTiff problem:
Can you send me the input you use with your graph?
Then I can try to reproduce it.
I’ll send you a PM where you can upload it to.

GiulioC · November 6, 2019, 12:56pm

I would like to report my experience in saving geotiff which produces a similar result of bad displaying in SNAP 7, which displays multiple repetitions of the real image.
I did some testings and to me this happens only when I save as GeoTIFF or GeoTIFF+XML an image with 9 bands (I tested from 5 to 10 bands). If I read the image with other software (e.g. QGIS or with gdal) it displays correctly, so it seems an error in SNAP reading the GeoTIFF.
However if I save in BigIFF format, the problem doesn’t occur (but it seems to be slower).